'\" t
.TH samtools-cat 1 "2 September 2022" "samtools-1.16.1" "Bioinformatics tools"
.SH NAME
samtools cat \- concatenate files together
.\"
.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
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.
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.SH SYNOPSIS
.PP
samtools cat
.RB [ -b
.IR list ]
.RB [ -h
.IR header.sam ]
.RB [ -o
.IR out.bam "] " in1.bam " " in2.bam " [ ... ]"

.SH DESCRIPTION
.PP
Concatenate BAMs or CRAMs. Although this works on either BAM or CRAM,
all input files must be the same format as each other. The sequence
dictionary of each input file must be identical, although this command
does not check this. This command uses a similar trick to
.B reheader
which enables fast BAM concatenation.

.SH OPTIONS
.TP 8
.BI "-b " FOFN
Read the list of input BAM or CRAM files from \fIFOFN\fR.  These are
concatenated prior to any files specified on the command line.
Multiple \fB-b\fR \fIFOFN\fR options may be specified to concatenate
multiple lists of BAM/CRAM files.
.TP 8
.BI "-h " FILE
Uses the SAM header from \fIFILE\fR.  By default the header is taken
from the first file to be concatenated.
.TP 8
.BI "-o " FILE
Write the concatenated output to \fIFILE\fR.  By default this is sent
to stdout.
.TP
.BI --no-PG
Do not add a @PG line to the header of the output file.
.TP
.BI "-@, --threads " INT
Number of input/output compression threads to use in addition to main thread [0].

.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.

.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
